What’s in your ‘html’?
Scripts would normally go in an initializer or be fired by an event in a component.
Calls to the plugin api would go in the initializer.
Changes to templates would probably be attached to a plugin connector (or if desperate only: override them in the templates folder)
You might also decorate or reopen widgets in the initializer.
You shouldn’t need to put ‘bare html’ anywhere, after all, what you are actually modifying is a web app, not a web page?
In any case there will no particular harm in running multiple plugins and TCs alongside each other …